Hybridization assays for the detection of campylobacter

ABSTRACT

A DNA probe and method for detecting Campylobacter jejuni, which consists essentially of a DNA sequence that is: 
     a) derived from a chromosomal sequence of a bacterium of the species C. jejuni or C. coli but is less than the entire chromosomal sequence of that bacterium; 
     b) capable of hybridizing to DNA of at least 80% of bacteria that are in the species C. jejuni and/or C. coli; and 
     c) not capable of hybridizing to DNA of bacteria that are not in the genus Campylobacter. The method features detecting C. jejuni in a sample by providing at least one probe capable of selectively binding to C. jejuni but not bacteria that do not belong to the genus Campylobacter, contacting that DNA probe with bacteria in the sample under conditions that allow the probe to hybridize to C. jejuni in the sample thus forming hybrid DNA complexes, and detecting the hybrid complexes as an indication of C. jejuni in the sample.

This is a divisional application of U.S. Ser. No. 06/692,778, filed on Jan. 17, 1985, and issued as U.S. Pat. No. 4,785,086 on Nov. 15, 1988.

BACKGROUND OF THE INVENTION

This invention relates to detecting bacteria of the species Campylobacter jejuni and Campylobacter coli. Throughout this application, when we refer to bacteria of the genus Campylobacter or of the species C. jejuni, C. coli, or C. fetus (or simply "C. jejuni", "C. coli", or "C. fetus", respectively) we mean bacteria that are so classified in Skerman et al, (1980) "Approved List of Bacterial Names" Int. J. Syst. Bacteriol. 30:225-420, By "C. jejuni", we mean to include bacteria described as C. fetus subsp. jejuni (but not other members of the species C. fetus) in Buchanan et al., The Shorter Bergey's Manual for Determinative Bacteriology (Williams & Wilkins 1982) in accordance with the classification in Skerman, supra and with the classification in a more recent edition of Bergey's Manual of Systematic Bacteriology (9th ed. 1984, vol. 1).

Detection of C. jejuni and C. coli is important in various medical contexts. For example, the presence of C. jejuni or C. coli in stool samples is indicative of gastroenteritis, and the ability to screen for their presence is useful in treating and controlling that disease. Detection of C. jejuni and C. coli in any possible transmission vehicle such as food is also important to avoid the spread of gastroenteritis.

Currently, the presence of C. jejuni and C. coli in stool samples is detected by cultivating an appropriately prepared sample on microbiological media under conditions favorable for growth of those bacteria. Those conditions include reduced oxygen tension and a temperature of about 42° C. The resulting colonies are then examined for morphological and biochemical characteristics, a process that typically takes at least three days and does not permit processing large numbers of samples.

Taber et al. U.S. Ser. No. 529,031 filed Sep. 2, 1983 discloses DNA probes for determining the presence of bacteria of the genus Salmonella in food.

Falkow U.S. Pat. No. 4,358,535 discloses a DNA probe for detecting Enterotoxigenic E. coli in clinical specimens.

SUMMARY OF THE INVENTION

In one aspect, the invention features a DNA probe consisting essentially of a DNA sequence that is:

a) derived from a chromosomal sequence of a bacterium of the species C. jejuni but is less than the entire chromosomal sequence of that C. jejuni;

b) capable of hybridizing to DNA of at least 80% of bacteria that are in the species C. jejuni; and

c) not capable of hybridizing to DNA of bacteria that are not in the genus Campylobacter. By a sequence that is "derived from a chromosomal sequence", we mean a sequence that is identical to that sequence, or a natural or engineered or synthetic variant that retains the desired function.

In another aspect, the invention features a method of detecting C. jejuni in a sample by providing at least one probe capable of selectively binding to DNA of C. jejuni but not to DNA of bacteria that do not belong to the genus Campylobacter, contacting that DNA probe with bacteria in the sample under conditions that allow the probe to hybridize to C. jejuni in the sample thus forming hybrid DNA complexes, and detecting the hybrid complexes as an indication of C. jejuni in the sample.

In a third aspect, the probe sequence is derived from, but is less than, an entire chromosomal sequence of C. coli, and it is capable of hybridizing to at least 80% of the bacteria of that species.

In preferred embodiments of the first aspect of the invention, the probe is also capable of binding to at least 80% of bacteria that are in the species C. coli. Most preferably in all aspects of the invention, the probe is capable of binding to at least 90% of the C. jejuni and 90% of the C. coli) so that it is used to detect the presence of either C. jejuni or C. coli in any given sample. Also in preferred embodiments, the probe is a HindIII fragment of a chromosome of a bacteria from the species C. jejuni or C. coli. The probe may be labeled using a label that is detectable, for example, a radioactive isotope such as ³² P or ¹²⁵ I incorporated in the probe by nick-translation or other means of labeling; alternatively the label binds selectively to an indicator comprising a binding partner and a chemical entity detectable, e.g. by fluorometric, immunological, electron microscopic or enzymatic methods. The label/binding partner pair may be avidin and biotin.

In preferred embodiments of the method, before contacting the probe with the bacterial DNA, the bacteria are separated from the sample and lysed to release their DNA, which then is denatured and immobilized on a binding support such as a nitrocellulose membrane. The sample may be food or a diagnostic sample, e.g. a stool sample. The probe also may be unlabeled, in which case the contacting and detecting steps are performed by sandwich hybridization (referred to in more detail below). One or more probes may be used in the method to increase its sensitivity.

In a fourth aspect, the invention features a DNA probe consisting essentially of fragments representing a total DNA preparation of C. jejuni, no detectable percentage of which is capable of hybridizing to bacteria that are not in the genus Campylobacter; a detectable percentage of the fragments will hybridize to the DNA of any given member of that genus. By the phrase "total DNA preparation," I mean DNA isolated by severing the chromosomal DNA to create various fragments that collectively represent substantially the entire chromosomal sequence. The DNA probe is used in a method comprising isolating fragments representing a total DNA preparation of C. jejuni and exposing the fragments to DNA of bacteria from a sample under conditions that allow hybridization.

In preferred embodiments of the fourth aspect, the C. jejuni used for the total DNA preparation is strain N941 (ATCC 39983), and the probe fragments are labeled.

The probe and detection method provide a reliable, fast, and straightforward means for detecting C. jejuni and C. coli--the two species of Campylobacter primarily implicated in gastroenteritis. So far as the inventors are aware, the probe does not depend on the ability to match a DNA probe with bacteria that e.g., express a specific protein, are pathenogenic, or possess any other phenotypical characteristic. Thus, the selectivity and utility of the probe is not limited to members of the species that exhibit a specific characteristic; nor is it dependent on locating the DNA responsible for a characteristic.

Our discovery that there is not just one, but a number, of specific probes provides the added advantage of increased sensitivity and signal amplification; the larger the number of different probes used, the greater the sensitivity of the assay. This is because when several different probes are used, each can hybridize to a different portion of a single bacterial chromosome so that the single chromosome bears multiple labels.

The assay of the invention gives rapid, accurate results. A fast and definitive result is important when determining a patient's therapeutic regime. When the detection method is used for food samples, its speed allows food manufacturers to reduce food storage time prior to shipment. In addition, the short time required to complete the test permits laboratories to handle large numbers of samples in a short period of time. Furthermore, the assay, depending only on the overall DNA sequences of the bacteria rather than their biochemical properties, can detect biochemically atypical as well as typical bacteria so that false negatives are avoided. The test requires no elaborate equipment and can be performed easily by personnel who have not had extensive technical training.

Finally, the recognition that it is possible to use a total DNA preparation without detectable hybridization to non-Campylobacter bacteria enables a ready source of easily prepared probes. A large number of fragments of the total DNA preparation can be expected to hybridize to any Campylobacter bacteria, providing extremely high sensitivity to such bacteria. Surprisingly, a total DNA preparation of C. jejuni does not provide false positive results, indicating that no detectable percentage of the chromosomal fragments hybridize to non-Campylobacter, and indicating that the amount of DNA homology between C. jejuni and other groups of bacteria is negligible.

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof and from the claims.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

Isolation of Probes.

A genomic library of C. jejuni DNA is constructed in a suitable plasmid or phage vector. A number of suitable vectors are available and have been described in Maniatis et al. (1982) Molecular Cloning, Cold Spring Harbor Laboratory. One such vector is pUN121 [Nilsson et al. (1983) Nucleic Acids Research 11:8019-8030]. The DNA from C. jejuni N941 (ATCC 39983) is digested with restriction endonuclease HindIII, creating fragments of different sizes. These fragments are then ligated into the HindIII site of a suitable vector using the general method described in Cohen et al., (1973) Proc. Nat'l Acad. Sci. 70:3240. This ligation mix is then used to transform E. coli HB101. The transformants are selected on the basis of a suitable marker. For example, when using the plasmid pUN121, the transformants can be selected on the basis of resistance to tetracycline. The transformants are then screened for the presence of plasmid DNA and independent transformants are examined by agarose gel electrophoresis. The plasmid DNA is transferred onto nitrocellulose membrane filters by the method of Southern described in Maniatis et al. (1982) cited above; and the DNA is probed with nick-translated E. coli DNA. The plasmids which do not hybridize to E. coli DNA (about 95%) are selected and purified by CsCl-ethidium bromide gradients. The insert DNA is purified from agarose gels after digestion with HindIII. These individual DNA fragments are then labeled with nick-translation and used as probes in testing C. jejuni or C. coli strains and also, enteric bacteria often found in feces as part of normal flora or as pathogens. Table 1 exemplifies the types of non-Campylobacter enteric bacteria that may be tested.

                  TABLE 1                                                          ______________________________________                                         ENTERIC BACTERIA USED IN SCREENING                                             Escherichia coli  Salmonella enteritidis                                       Enterobacter cloacae                                                                             Salmonella serotype Cl                                       Enterobacter agglomi                                                                             Salmonella typhimurium                                       Enterabacter gergoviae                                                                           Serratra liquefaciens                                        Citrobacter forundii                                                                             Serratia marcescens                                          Citrobacter diversus-levihea                                                                     Shigella flexneri                                            Klebsiella pneumoniae                                                                            Shigella sonneii                                             Klebsiella oxytoca                                                                               Shigella byoydii                                             Proteus mirabilis Shigella dysenteriae                                         Proteus morganii  Vibrio parahaemolyticus                                      Proteus rettgeri                                                               ______________________________________                                    

Strains of C. jejuni and C. coli that can be used in the above screening procedure are available from numerous sources, particularly from major medical centers. For example, well-characterized C. jejuni and C. coli strains are available from the University of Massachusetts Medical Center in Worcester, Mass. c/o Gary Doren.

C. jejuni and C. coli strains are also available from Scott Laboratories, Inc., Fiskville, R.I. In addition, various clinically isolated strains are available from Scott Laboratories. Other sources of clinical isolates include the Veterns Administration Medical Center, Denver, Colo. (M. J. Blaser) and Vermont Department of Public Health, Burlington, Vt. (Tanya Sandros).

By way of example, Table 2 lists eight specific probes identified by their inability to hybridize with DNA of the species listed in Table 1 and their ability to hybridize with a high percentage of 98 distinct Campylobacter strains.

                  TABLE 2                                                          ______________________________________                                         LIST OF CAMPYLOBACTER SPECIFIC                                                 PROBES AND THEIR PROPERTIES                                                                            Percentage of                                          Probe      Size (b)     Strains Detected                                       ______________________________________                                         CJ12A      960          100%                                                   CJ29B      970          85%                                                    CJ41A      2150         91%                                                    CJ41B      2 fragments:                                                                   1250 and 1300 b.p.                                                                          93%                                                    CJ44A      2 fragments:                                                                   2650 and 3000 b.p.                                                                          99%                                                    CJ44B      1700         99%                                                    CJ59       1500         90%                                                    CJ87A      1200         96%                                                    ______________________________________                                    

The four preferred probes have been deposited with the NRRL located in Peoria, Ill. and bear the following accession numbers

    ______________________________________                                                Probe        NRRL No.                                                   ______________________________________                                                CJ12A        B 15911                                                           CJ29B        B 15912                                                           CJ59         B 15913                                                           CJ87A        B 15914                                                    ______________________________________                                    

With respect to these probes and the above-mentioned ATCC deposit of C. jejuni, N941, applicants' assignee, Integrated Genetics, Inc., acknowledges its responsibility to replace these cultures should they die before the end of the term of a patent issued hereon, and its responsibility to notify the depository of the issuance of such a patent, at which time the deposits will be made available to the public. Until that time the deposits will be made available to the Commissioner of Patents under the terms of 37 CFR Section 1.14 and 35 USC Section 112.

Construction, Labeling, and Use of Probes.

Probes may be constructed from the isolates of Table 2 as described by Taber and Fitts, U.S. Pat. No. 4,689,295, filed Sep. 2, 1983, which is hereby incorporated by reference. DNA is labeled by nick-translation according to known methods or by other known methods of labeling such as primer extension, or by the non-isotopic methods described by Landes U.S. Pat. No. 4,626,501 filed Sep. 2, 1983, which is hereby incorporated by reference. U.S. Pat. No. 4,689,295 and U.S. Pat. No. 4,626,501 also describe apparatus and methods for the use of probes that have been so labeled. Specifically, those skilled in the art will recognize that it is possible to adjust hybridization conditions such as temperature (e.g. 55°-70° C.) ionic strength (1M NaCl), and other factors (e.g. the addition of formamide) to provide varying selectivity and sensitivity levels.

Detection of C. Jejuni in Stools.

Stool samples from healthy individuals may be screened with each of the DNA probes CJ12A, CJ29B, CJ44A, CJ59 and CJ87A and also using a mixture of probes. The hybridization may be performed as described in the above-referenced U.S. Pat. No. 4,689,295 on stool samples which are directly spotted on nitrocellulose membrane filters as well as samples which are inoculated on selective plates as described by Blaser et al., (1979) Ann. Intern. Med. 91:179 and on non-selective plates. In all cases, the stool from healthy individuals shows no hybridization to the DNA probes, confirming previous studies showing that healthy individuals do not have any detectable C. jejuni in their stools. (M. B. Skirrow, 1982, J. Hyg. Camb., 89:175). Stool specimens that include C. jejuni are detectable in the stool samples. When radioactivity labeled probes are used to evaluate samples immobilized on filters, exposure of the filters to X-ray film will exhibit a dark spot for samples containing C. jejuni or C. coli.

Total DNA Probe.

An extraordinarily sensitive DNA probe can be prepared from the DNA of a member of the species C. jejuni. Specifically, a total DNA preparation is produced from a strain of C. jejuni such as N941, discussed above. Any of a number of known techniques may be used for that purpose. For example, Maniatis, cited above, cites suitable procedures for isolating bacterial DNA. These isolation procedures fragment the bacterial chromosome which is about 4,000 k.b. (assuming that the E. coli and C. jejuni chromosomes are comparable in size) to yield isolated fragments of about 10-20 kb. These fragments are then labeled by any of the procedures discussed above such as nick translation, further fragmenting the DNA to an average size of about 500-1000 bp. These fragments are a suitable size for a probe and, surprisingly, they exhibit no detectable hybridization with non-Campylobacter when subjected to the hybridization procedures discussed above. At the same time, the probe is extremely sensitive because hybridization can take place at many locations on the same Campylobacter chromosome due to the presence of numerous distinct labeled fragments.

OTHER EMBODIMENTS

Other embodiments are within the following claims. For example, other labeling methods may be used. Unlabeled probes may be used, in which case a sandwich hybridization is used according to known techniques such as the one described in European Patent Application EPO 079139A1. The number of probes required depends in part on the sensitivity required in a given application and the tolerance for false negative results. In general, one or more probes may be used. Synthetically constructed DNA sequences as well as pieces of the genome of naturally occurring C. jejuni or C. coli cab be used as probes.

Other clinical samples may be tested--for example, gastric juices or intestinal contents. Food may be tested as described in Taber and Fitts U.S. Pat. No. 4,689,295 cited above. 

We claim:
 1. A method for specifically detecting bacteria that are in the genus Campylobacter in a sample, said method comprising the steps of:providing at least one DNA probe consisting of the entire C. jejuni genome or a fragment resulting from a restriction digest of the entire C. jejuni genome; further providing a sample; treating said sample to lyse any bacteria present therein and to release DNA contained within said bacteria; further treating said released DNA to form single-stranded DNA; contacting said DNA probe with said single-stranded DNA from lysed bacteria in said sample under selective hybridization conditions that allow said probe to hybridize to single-stranded Campylobacter DNA in said sample, if present, thus forming hybrid DNA complexes, and not to hybridize to non-Campylobacter DNA; and detecting said hybrid complexes as an indication of Campylobacter in said sample.
 2. The method of claim 1, wherein said method detects the presence of one or both of C. jejuni and C. coli if present in said sample, said contacting step comprises contacting said probe with any lysed bacteria in said sample under selective hybridization conditions that allow said probe to hybridize to C. jejuni or C. coli DNA, and not to hybridize to non-C. jejuni or C. coli DNA, and said detecting step comprises detecting hybrid DNA complexes as an indication of C. jejuni or C. coli in said sample.
 3. The method of claim 1 wherein said probe is labeled and said detecting step comprises detecting said label or detecting an indicator to which said label selectively binds.
 4. The method of claim 1 wherein, prior to contacting sample bacteria with said probe, said bacteria are separated out of said sample and lysed to release their DNA, said DNA then being denatured and immobilized on a DNA binding support.
 5. The method of claim 4 wherein said DNA binding support comprises a nitrocellulose membrane.
 6. The method of claim 1 wherein at least two DNA probes are employed.
 7. The method of claim 1 wherein said method further comprises contacting said single-stranded DNA from lysed bacteria with a second probe wherein one of said probe or said second probe is detectable, and the other of said probe or said second probe is immobilized on a solid phase, whereby sandwich hybridization may be effected.
 8. The method of claim 1 wherein said sample is a gastroenteric sample.
 9. The method of claim 1 wherein said sample is a stool sample.
 10. The method of claim 1 wherein said sample is a food sample.
 11. The method of claim 1 wherein said probe is selected from the group consisting of:a) the probe deposited under accession number NRRL B 15911; b) the probe deposited under accession number NRRL B 15912.; c) the probe deposited under accession number NRRL B 15913; d) the probe deposited under accession number NRRL B 15914; and e) combinations of two or more of a), b), c), and d). 